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How well theoretically motivated is $R$-parity?

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I understand that $R$-parity is empirically necessary in order to avoid proton decay, but theoretically I'm worried that it amounts to a tune or "hack" that spoils the naturalness argument for supersymmetry. In other words, TeV scale supersymmetry solves the hierarchy problem, but isn't it unnatural to pick one out of a very large space of possible symmetries in order to patch-up the proton decay problem? Is $B-L$ symmetry somehow natural to expect theoretically (wikipedia mentions something vague about it arising naturally in $SO(10)$ GUTs)?

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